Active sites convergent evolution

All the four essential features of the active site of chymotrypsin are thus also present in subtilisin. Furthermore, these features are spatially arranged in the same way in the two enzymes, even though different framework structures bring different loop regions into position in the active site. This is a classical example of convergent evolution at the molecular level. 

Serine proteinases such as chymotrypsin and subtilisin catalyze the cleavage of peptide bonds. Four features essential for catalysis are present in the three-dimensional structures of all serine proteinases a catalytic triad, an oxyanion binding site, a substrate specificity pocket, and a nonspecific binding site for polypeptide substrates. These four features, in a very similar arrangement, are present in both chymotrypsin and subtilisin even though they are achieved in the two enzymes in completely different ways by quite different three-dimensional structures. Chymotrypsin is built up from two p-barrel domains, whereas the subtilisin structure is of the a/p type. These two enzymes provide an example of convergent evolution where completely different loop regions, attached to different framework structures, form similar active sites. 

Mattevi, A., Vanoni, M. A., Todone, F., Rizzi, M., Teplyakov, A., Coda, A., Bolognesi, M., and Curti, B., 1996, Crystal structure of D-amino acid oxidase a case of active site mirror-image convergent evolution with flavocytochrome Proc. Natl. Acad. Sci. USA. 93 7496n7501. 

A third family, the -carbonic anhydrases, also has been identified, initially in the archaeon Methanosarcina thermophila. The crystal structure of this enzyme reveals three zinc sites extremely similar to those in the a-carbonic anhydrases. In this case, however, the three zinc sites lie at the interfaces between the three subunits of a trimeric enzyme (Figure 9.31). The very striking left-handed P-helix (a P strand twisted into a left-handed helix) structure present in this enzyme has also been found in enzymes that catalyze reactions unrelated to those of carbonic anhydrase. Thus, convergent evolution has generated carbonic anhydrases that rely on coordinated zinc ions at least three times. In each case, the catalytic activity appears to be associated with zinc-bound water molecules. 

Other proteases employ the same catalytic strategy. Some of these proteases, such as trypsin and elastase, are homologs of chymotrypsin. In other proteases, such as subtilisin, a very similar catalytic triad has arisen by convergent evolution. Active-site structures that differ from the catalytic triad are present in a number of other classes of proteases. These classes employ a range of catalytic strategies but, in each case, a nucleophile is generated that is sufficiently powerful to attack the peptide carbonyl group. In some enzymes, the nucleophile is derived from a side chain whereas, in others, an activated water molecule attacks the peptide carbonyl directly. 

Many of the enzymes that catalyze these reactions, such as serine hy- droxymethyltransferase, which converts serine into glycine, have the same fold as that of aspartate aminotransferase and are clearly related by divergent evolution. Others, such as tryptophan synthetase, have quite different overall structures. Nonetheless, the active sites of these enzymes are remarkably similar to that of aspartate aminotransferase, revealing the effects of convergent evolution. 

This catalytic site resembles that of DNA polymerase (Secion 27.2.2) in that it includes two metal ions in its active form (Figure 28.2). One metal ion remains bound to the enzyme, whereas the other appears to come in with the nucleoside triphosphate and leave with the pyrophosphate. Three conserved aspartate residues of the enzyme participate in binding these metal ions. Note that the overall structures of DNA polymerase and RNA polymerase are quite different their similar active sites are the products of convergent evolution. 

Figure 6.17 Convergent evolution of protease active sites. The relative positions of the three key residues shown are nearly identical in the active sites of the serine proteases chymotrypsin and subtilisin.

Other enzymes that are not homologs of chymotrypsin have been found to contain very similar active sites. As noted in Chapter 6, the presence of very active sites in these different protein families is a consequence of convergent evolution. Subtilisin, a protease in bacteria such as Bacillus amyloliq-uejadens, is a particularly well characterized example. The active site of this enzyme includes both the catalytic triad and thcoxyanion hole. However, one NH groups that forms the oxyanion hole comes from the side chain of an asparagine residue rather than from the peptide backbone (Figure 9.14). 

Convergent Evolution Has Generated Zinc-Based Active Sites in Different Carbonic Anhydrases... 

DNA polymerases are remarkably similar in overall shape, although they differ substantially in detail. At least five structural classes have been identified some of them are clearly homologous, whereas others are probably the products of convergent evolution. In all cases, the finger and thumb domains wrap around DNA and hold it across the enzyme s active site, which comprises residues primarily from the palm domain. Furthermore, all DNA polymerases use similar strategies to catalyze the polymerase reaction, making use of a mechanism in which two metal ions take part. 

When we look at convergence at the biochemical level, we can further document the general question of evolution in the life sciences. Convergent evolution is manifest at the active sites of enzymes and in whole proteins, as well as in the genome itself, as the following examples show. 

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